From: venkata agasthya (kvagasthya_at_gmail.com)
Date: Wed Jul 24 2013 - 15:12:06 CDT
Hello everyone,
I have mailed in this group before about my problem with minimizing the
energy of a protein/water system. I have tried running the minimization
script using 500, 1000 and 10000 steps but the run gets stuck at a
particular step and doesn't continue. It reaches a certain step and get's
stuck. do anyone know why this happens.
This is my minimization config file
###################################################
# ESTROGEN RECEPTOR:
###################################################
# MD SETUP
timestep 2.0
numsteps 1000
# FLEXIBLE CELL
useflexiblecell no
# PSF
structure protein.psf
# FORCE FIELD
parameters /work/agasthya/testing/par_all27_prot_lipid.prm
paraTypeCharmm on
# INPUT
coordinates protein.pdb
# PBC
CellBasisVector1 50 0 0
CellBasisVector2 0 50 0
CellBasisVector3 0 0 50
CellOrigin 0 0 0
# OUTPUT
outputenergies 100
outputtiming 100
outputpressure 100
restartfreq 100
XSTFreq 100
outputname minimization_0
restartname minimization
binaryrestart yes
binaryoutput no
# PME
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSpacing 1
# WRAP
wrapAll on
# CONSTANT-T
temperature 300.0
langevin on
langevinTemp 300.0
langevinDamping 1.0
# CONSTANT-P
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 75
LangevinPistonDecay 25
LangevinPistonTemp 300
StrainRate 0.0 0.0 0.0
useGroupPressure yes
# SPACE PARTITIONING
splitpatch hydrogen
hgroupcutoff 2.8
stepspercycle 20
margin 1.0
# CUT-OFFS
switching on
switchdist 8.0
cutoff 9.0
pairlistdist 10.0
# RESPA
#fullElectFrequency 2
#nonbondedFreq 1
# 1-4 NON-BONDED
exclude scaled1-4
1-4scaling 1.0
# COM
commotion no
# SHAKE
rigidbonds all
rigidtolerance 0.000001
rigiditerations 400
# MINIMIZATION
minimize 1000
Thanks,
Agasthya.
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